Since the beginning of the 20th Century, it is known that infections could play a role in cancer, with 18-20% of cancers associated with infectious agents. This could be relatively higher in developing countries like India. Our team at ACTREC-Tata Memorial Centre developed a highly sensitive and specific automated computational tool HPVDetector to quantify the presence of human papillomavirus (HPV). This was done by subtracting human sequences from the cancer genome and comparing the rest with the HPV genome to identify the presence of HPV sequence trace and determine the range of all co-infecting HPV strains in the same individual.
The analysis revealed significant occurrence of HPV 16, 18, and 31, among others, in cervical cancer. But a surprising finding was that Indian patients with oral tumours showing a distinct tobacco usage gene signature were devoid of HPV infection. This was in sharp contrast to the oral tumours among Caucasian patients, wherein tobacco genetic signature is not common but is marked by a significant presence of HPV. Several groups have corroborated this finding, and it is well established that oral tumours among Indian patients are not driven by HPV infection.
In this study published on Mar 4, in NAR Cancer, Sanket Desai, the lead researcher from the group, developed another advanced automated computational tool — Infectious Pathogen Detector (IPD). Beyond HPV, IPD can detect the presence of 1,058 pathogens in the human cancer genome from datasets generated from any Next Generation Sequencing platform. This tool is publicly available for download from the ACTREC- TMC website. Using IPD, the DNA and RNA sequence from 1,407 cancer samples of oral, breast, cervical, gall bladder, lung and colorectal tumours derived from Indians were analysed and compared with Caucasian patients.
